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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgactattacaacaaatacccctagtttataattctttgttgatcttgttttgctatcaaagtcttatcaggaacatatgtttttttaatttcaccttcttaaagagcttagcctgaatcttttaattttgcagGCTGGATATCTTGATATATGGGAACCAGCTACTTTGGCCATTAAGAGGGAAGGTTACAGCATCAAGTGTACTGGACCTAGTGGTGCTGTAGTCTCTGAGA

Basic information

species Vitis vinifera
transcript Vv07s0130g00420.t01
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0130g00420.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: LOC_Os01g01800.1 (Oryza sativa), 3'ss of exon 17
gtatgactattacaacaaatacccctagtttataattctttgttgatcttgttttgctatcaaa-gtcttatcaggaacatatgtttttttaatttcaccttcttaaagagcttagcctgaatcttttaattttgcagGCTGGATATCTTGATATATGGGAACCAGCTACTTTGGCCATTAAGAGGGAAGGTTACAGCATCAAGTGTACTGGACCTAGTGGTGCTGTAGTCTCTGAGA
                              |||  |||| | ||  |     ||  |||||||| |  || |||  ||  | |  |  ||| ||   |   | | |||          | |||||| | ||   |||||    || | | ||||| ||||||||||||| |||||| || ||||||||||| ||||| || || |||||||| |   |||||| |||  || | |   
-----------------------------gtatg-ttctctattacttggaattatctatcaaaagcattctcactaatttcttatgatttcatgcaattatttcaaatg-------ttaaatcttcttata--gCAGGTGAAATTTTTAGATATGTGGGAACCAGCTATTTTGGCAATAAAGAGGGAAGGCTACAGTATTAAATGTACTGGTCAGCGTGGTGTTGTTCTCACAG---

upper sequence: Vv07s0130g00420.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: LOC_Os01g01800.2 (Oryza sativa), 3'ss of exon 17
gtatgactattacaacaaatacccctagtttataattctttgttgatcttgttttgctatcaaa-gtcttatcaggaacatatgtttttttaatttcaccttcttaaagagcttagcctgaatcttttaattttgcagGCTGGATATCTTGATATATGGGAACCAGCTACTTTGGCCATTAAGAGGGAAGGTTACAGCATCAAGTGTACTGGACCTAGTGGTGCTGTAGTCTCTGAGA
                              |||  |||| | ||  |     ||  |||||||| |  || |||  ||  | |  |  ||| ||   |   | | |||          | |||||| | ||   |||||    || | | ||||| ||||||||||||| |||||| || ||||||||||| ||||| || || |||||||| |   |||||| |||  || | ||||
-----------------------------gtatg-ttctctattacttggaattatctatcaaaagcattctcactaatttcttatgatttcatgcaattatttcaaatg-------ttaaatcttcttata--gcagGTGAAATTTTTAGATATGTGGGAACCAGCTATTTTGGCAATAAAGAGGGAAGGCTACAGTATTAAATGTACTGGTCAGCGTGGTGTTGTTCTCACAGAGA

upper sequence: Vv07s0130g00420.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: LOC_Os05g01060.1 (Oryza sativa), 3'ss of exon 17
gtatgactattacaacaaatacccctagtttataattctttgttgatcttgttttgctatcaaagtcttatcaggaacatatgtttttttaatttcaccttcttaaagagcttagcctgaatcttttaattttgcagGCTGGATATCTTGATATATGGGAACCAGCTACTTTGGCCATTAAGAGGGAAGGTTACAGCATCAAGTGTACTGGACCTAGTGGTGCTGTAGTCTCTGAGA
                                         ||   |  | |||   | | | | |  |||    | |||    | |    |     | ||  |    |  | | | |    || | ||| ||||||| | | | ||| ||||| ||||||||||||   ||||| || |||||||||||||||||||| ||||||| ||| |   |||||| |||  |  | || |
-----------------------------------------gtatgttatatttcctttttatattgatatgtcaatcat----tctcacgacacttcttttgttgtcatataaccattggactatcaatcttgcagGTTAGGTTTCTAGATATGTGGGAACCAGCTGTATTGGCAATAAAGAGGGAAGGTTACAGCATTAAGTGTAATGGCCAGCGTGGTGTTGTTATTACAGAAA

upper sequence: Vv07s0130g00420.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GRMZM2G104377_T03 (Zea mays), 3'ss of exon 16
gtatgactattacaacaaatacccctagtttataattctttgttgatcttgttttgctatcaaagtcttatcaggaacatatgtttttttaatttcaccttcttaaagagcttagcctgaatcttttaattttgcagGCTGGATATCTTGATATATGGGAACCAGCTACTTTGGCCATTAAGAGGGAAGGTTACAGCATCAAGTGTACTGGACCTAGTGGTGCTGTAGTCTCTGAGA
                                        | |    |   || | ||   |  ||||| ||| || ||  | ||| | |   ||  | || | | |   |   |     |||   | ||| |||||| | ||| | | ||||| ||||||||||||| |||||| || |||||||||||||||||| | ||||||| |||||   | ||||  || |||   ||||
---------------------------------------gtatgtccccaattcttctcaaatggtctt-tcaagagcac-tctttctatgtctttccattatcatatgaccctgtgaacatcaaattattctgcagGTTAGATTTTTAGATATGTGGGAACCAGCTATTTTGGCAATAAAGAGGGAAGGTTACAGCGTTAAGTGTAATGGACAGCGCGGTGTCGTTGTCATGGAGA

upper sequence: Vv07s0130g00420.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GLYMA10G31880.1 (Glycine max), 3'ss of exon 18
gtatgactattacaacaaatacccctagt-ttataattctttgttgatcttgttttgctatcaaagtcttatcaggaacatatgtttttttaatttcaccttcttaaagagcttagcctgaatctt---ttaattttgcagGCTGGATATCTTGATATATGGGAACCAGCTACTTTGGCCATTAAGAGGGAAGGTTACAGCATCAAGTGTACTGGACCTAGTGGTGCTGTAGTCTCTGAGA
|||   | || | |  |  |  |   | | |||| | | |   | ||     | ||| | ||||  | ||||       ||  || || || ||       || |||     |||     | | ||   || || || ||| |||||||||||||||||||||||||||| || ||| ||||||||||||||||||| || ||||| || | |||||| | |||   |||| || | || |
gtaattcaatgaaagtagttttcttaattgttatgaatttccttcga----atgttggtgtcaa--tattattttacctattagtcttctttatgaagaactcctaacagttttataaatatttttggcttgatattacagACTGGATATCTTGATATATGGGAACCAGCGACATTGACCATTAAGAGGGAAGGTTATAGTATCAAATGCAGTGGACCAAATGGATTTGTAATCACAGAAA

upper sequence: Vv07s0130g00420.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GLYMA20G35770.4 (Glycine max), 3'ss of exon 18
gtatgactattacaacaaatacccctagtt--tataattctttgttgatcttgttttgctatcaaagtcttatcaggaacatatgtttttttaatttcaccttcttaaagagcttagcctgaatctt---ttaattttgcagGCTGGATATCTTGATATATGGGAACCAGCTACTTTGGCCATTAAGAGGGAAGGTTACAGCATCAAGTGTACTGGACCTAGTGGTGCTGTAGTCTCTGAGA
|||    || |  ||  | |   | || ||  ||| | | | | | ||     | ||  | ||||| | ||||  |   |||  || || || ||       || |||     |||     | | ||   || || || ||| || ||||||||||||||||||| ||||| || |||||||||| ||||||||||||||| ||||| || | |||||  ||||| | |||| || | || |
gta-atttaatgaaagtagttttcttaattgttatgaatttctttcga----atgttagtgtcaaaatattatttgacccatcagtcttctttatgaagaactcctaactgttttataaatatttttggcttgatattacagACTAGATATCTTGATATATGGGAGCCAGCCACATTGGCCATTACGAGGGAAGGTTACAGTATCAAATGCAGTGGACAAAGTGGAGTTGTAATCACAGAAA

upper sequence: Vv07s0130g00420.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: AT5G23490.1 (Arabidopsis thaliana), 3'ss of exon 17
gtatgactattacaacaaatacccctagtttataattctttgttgatcttgttttgctatcaaagtcttatcaggaacatatgtttttttaatttcaccttcttaaagagcttagcctgaatcttttaattttgcagGCTGGATATCTTGATATATGGGAACCAGCTACTTTGGCCATTAAGAGGGAAGGTTACAGCATCAAGTGTACTGGACCTAGTGGTGCTGTAGTCTCTGAGA------
                                             ||    |||  |  |  || || | |    | | |||||| | |     |   |||      |   | | |||   ||   |   |   |||| ||| |   | |||||||||||| |||| || ||  | |||||||| |||||||||||||||||||||| |      |||| |     | |  | || |      
-------------------------------------------gtataacatttaccatttcaactcgtttatttagcctatgttctctctggcttttctt------ggattaatcct---tcacatgcatggacagGTTGGCTTCGTGGATATATGGGAAGCAGCAACATTATCTATTAAGAGAGAAGGTTACAGCATCAAGTGTATT------AGTGATCTCACAATTGCAGAAAAGTTCT

upper sequence: Vv07s0130g00420.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: AT5G23510.1 (Arabidopsis thaliana), 3'ss of exon 6
gtatgactattacaacaaatacccctagtttataattctttgttgatcttgttttgctatcaaagtcttatcaggaacatatgtttttttaatttcaccttcttaaagagcttagcctgaatcttttaattttg--cagGCTGGATATCTTGATATATGGGAACCAGCTACTTTGGCCATTAAGAGGGAAGGTTACAGCATCAAGTGTACTGGACCTAGTGGTGCTGTAGTCTCTGAGA------
                                                         ||||| | | |       |||   | | ||||   | |    | |||  |    |    |  |  | | |   ||||   ||  ||| |   |  ||||||||||| ||||||| ||  | ||| |||| |||||||||| ||||||||||| |      |  | |     | |  | || |      
--------------------------------------------------------gtatcacattttctgtttcaactcgtatattttggctatgttttccttggattaatccttcacatgcatgtggctttggatagATTGGTTTCGTGCATATATGGGAAGCAGCTACGTTATCTATTGAGAGAGAAGGTTACACCATCAAGTGTAAT------AACGATCTCACAATTACAGAAAAGTTCT

upper sequence: Vv07s0130g00420.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: AT5G08440.2 (Arabidopsis thaliana), 3'ss of exon 18
gtatgactattacaacaaatacccctagtttataattctttgttgatcttgttttgctatcaaagtcttatcaggaacatatgtttttttaatttcaccttcttaaagagcttagcctgaatcttttaattttgcagGCTGGATATCTTGATATATGGGAACCAGCTACTTTGGCCATTAAGAGGGAAGGTTACAGCATCAAGTGTACTGGACCTAGTGGTGCTGTAGTCTCTGAGA------
||||| | | | |    | | |  ||  |||| || |||  ||   | | ||||| ||    |   ||  ||      |     |   ||     |   ||  |      ||  ||  ||    | | ||    |||  ||| ||| | |||||||||||| ||||||| ||| | |||||||  ||||| |||||||||||   ||||      | ||   ||||| |  | || |      
gtatg-ccacttctcttatttcatct--tttacaaatctg-gtc--tttggttttcctgcacatacctcctctatgttactctctcacttgtgcgcctattgcttttttactatgc--gatctctcttatgaaacagATTGGTTATTTGGATATATGGGAAGCAGCTACATTGTCTATTAAGAAAGAAGGCTACAGCATCAAACCTACT------AATGACCCTGTAATTACAGAAAAGTTCT

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|30130582|gb|CB915921.1|CB915921
EST:     TAGAGAAGACCCTTGTTACTGGTCATACTTCATACAAAGTATCCCTGTCG                         GCTGGATATCTTGATATATGGGAACCAGCTACTTTGGCCATTAAGAGGGAA
genomic: TAGAGAAGACCCTTGTTACTGGTCATACTTCATACAAAGTATCCCTGTCGgtatgactat ... aattttgcagGCTGGATATCTTGATATATGGGAACCAGCTACTTTGGCCATTAAGAGGGAA
EST: gi|110360360|gb|EC923401.1|EC923401
EST:     TAGAGAAGACCCTTGTTACTGGTCATACTTCATACAAAGTATCCCTGTCG                         GCTGGATATCTTGATATATGGGAACCAGCTACTTTGGCCATTAAGAGGGAA
genomic: TAGAGAAGACCCTTGTTACTGGTCATACTTCATACAAAGTATCCCTGTCGgtatgactat ... aattttgcagGCTGGATATCTTGATATATGGGAACCAGCTACTTTGGCCATTAAGAGGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttttttaatttcaccttcttaaagagcttagcctgaatcttttaattttgcagGCTGGATATCTTGATATATGGGAACCAGCTACTTTGGCCATTAAGAGGGAAGGTTACAGCATCAAGTGTACTGGACCTAGTGGTGCTGTAGTCTCTGAGA
                                         ttttaat  putative branch site (score: 3)
                                       tctttta  CT-rich tract
                                   tgaatcttttaatttt  TA-rich tract